Difference between revisions of "FAQ"
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| − | + | === Using geWorkbench === | |
| − | Q. I get a Java error when I try to start geWorkbench. | + | ====Q. I get a Java error when I try to start geWorkbench.==== |
A. This is almost always caused by the Sun Java 1.5 JRE not being installed or not being found. Try reinstalling the Java 1.5 JRE and then reinstall geWorkbench. geWorkbench must be installed after the JRE. | A. This is almost always caused by the Sun Java 1.5 JRE not being installed or not being found. Try reinstalling the Java 1.5 JRE and then reinstall geWorkbench. geWorkbench must be installed after the JRE. | ||
| − | Q. How do I increase the amount of memory available to Java to run geWorkbench? | + | ====Q. How do I increase the amount of memory available to Java to run geWorkbench?==== |
A. If you are running a packaged distribution of geWorkbench (created using InstallAnywhere), there is a file in the geWorkbench root directory called UILauncher.lax. There is a line there which specifies the Java heap size: | A. If you are running a packaged distribution of geWorkbench (created using InstallAnywhere), there is a file in the geWorkbench root directory called UILauncher.lax. There is a line there which specifies the Java heap size: | ||
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| − | Q. ARACNE does not run in version 1.0.4 (Note that this version has been superseded). | + | ====Q. ARACNE does not run in version 1.0.4 (Note that this version has been superseded).==== |
A. There were two text files that were omitted from the distribution, you can download them from the [[Tutorial_-_ARACNE|ARACNE tutorial]] page and install them into the geWorkbench root directory. | A. There were two text files that were omitted from the distribution, you can download them from the [[Tutorial_-_ARACNE|ARACNE tutorial]] page and install them into the geWorkbench root directory. | ||
| − | Q. ARACNE is not included in geWorkbench 1.0.5. How can I run this algorithm? | + | ====Q. ARACNE is not included in geWorkbench 1.0.5. How can I run this algorithm?==== |
A. A new, Java-based version of ARACNE has been implemented in the development version of geWorkbench. You can download the development version of geWorkbench from the GForge site (http://gforge.nci.nih.gov/scm/?group_id=78). Use the "Nightly CVS Tree Snapshot" link. However, this is a source distribution which you will need to compile yourself (requiring Java JDK 5 and Ant). | A. A new, Java-based version of ARACNE has been implemented in the development version of geWorkbench. You can download the development version of geWorkbench from the GForge site (http://gforge.nci.nih.gov/scm/?group_id=78). Use the "Nightly CVS Tree Snapshot" link. However, this is a source distribution which you will need to compile yourself (requiring Java JDK 5 and Ant). | ||
A standalone version of ARACNE is also availabe at http://amdec-bioinfo.cu-genome.org/html/ARACNE.htm | A standalone version of ARACNE is also availabe at http://amdec-bioinfo.cu-genome.org/html/ARACNE.htm | ||
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Revision as of 17:08, 30 April 2007
Contents
- 1 Using geWorkbench
- 1.1 Q. I get a Java error when I try to start geWorkbench.
- 1.2 Q. How do I increase the amount of memory available to Java to run geWorkbench?
- 1.3 Q. ARACNE does not run in version 1.0.4 (Note that this version has been superseded).
- 1.4 Q. ARACNE is not included in geWorkbench 1.0.5. How can I run this algorithm?
Using geWorkbench
Q. I get a Java error when I try to start geWorkbench.
A. This is almost always caused by the Sun Java 1.5 JRE not being installed or not being found. Try reinstalling the Java 1.5 JRE and then reinstall geWorkbench. geWorkbench must be installed after the JRE.
Q. How do I increase the amount of memory available to Java to run geWorkbench?
A. If you are running a packaged distribution of geWorkbench (created using InstallAnywhere), there is a file in the geWorkbench root directory called UILauncher.lax. There is a line there which specifies the Java heap size:
- LAX.NL.JAVA.OPTION.JAVA.HEAP.SIZE.MAX
lax.nl.java.option.java.heap.size.max=640678989
Here it is shown set to about 640 MB. You can experiment with increasing this, subject to the amount of memory in your machine and demands on it from other applications.
Q. ARACNE does not run in version 1.0.4 (Note that this version has been superseded).
A. There were two text files that were omitted from the distribution, you can download them from the ARACNE tutorial page and install them into the geWorkbench root directory.
Q. ARACNE is not included in geWorkbench 1.0.5. How can I run this algorithm?
A. A new, Java-based version of ARACNE has been implemented in the development version of geWorkbench. You can download the development version of geWorkbench from the GForge site (http://gforge.nci.nih.gov/scm/?group_id=78). Use the "Nightly CVS Tree Snapshot" link. However, this is a source distribution which you will need to compile yourself (requiring Java JDK 5 and Ant).
A standalone version of ARACNE is also availabe at http://amdec-bioinfo.cu-genome.org/html/ARACNE.htm
